fix bond/break command

Syntax

fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...
  • ID, group-ID are documented in fix command

  • bond/break = style name of this fix command

  • Nevery = attempt bond breaking every this many steps

  • bondtype = type of bonds to break

  • Rmax = bond longer than Rmax can break (distance units)

  • zero or more keyword/value pairs may be appended to args

  • keyword = prob

    prob values = fraction seed
      fraction = break a bond with this probability if otherwise eligible
      seed = random number seed (positive integer)
    

Examples

fix 5 all bond/break 10 2 1.2
fix 5 polymer bond/break 1 1 2.0 prob 0.5 49829

Description

Break bonds between pairs of atoms as a simulation runs according to specified criteria. This can be used to model the dissolution of a polymer network due to stretching of the simulation box or other deformations. In this context, a bond means an interaction between a pair of atoms computed by the bond_style command. Once the bond is broken it will be permanently deleted, as will all angle, dihedral, and improper interactions that bond is part of.

This is different than a pairwise bond-order potential such as Tersoff or AIREBO which infers bonds and many-body interactions based on the current geometry of a small cluster of atoms and effectively creates and destroys bonds and higher-order many-body interactions from timestep to timestep as atoms move.

A check for possible bond breakage is performed every Nevery timesteps. If two bonded atoms I,J are further than a distance Rmax of each other, if the bond is of type bondtype, and if both I and J are in the specified fix group, then I,J is labeled as a “possible” bond to break.

If several bonds involving an atom are stretched, it may have multiple possible bonds to break. Every atom checks its list of possible bonds to break and labels the longest such bond as its “sole” bond to break. After this is done, if atom I is bonded to atom J in its sole bond, and atom J is bonded to atom I in its sole bond, then the I,J bond is “eligible” to be broken.

Note that these rules mean an atom will only be part of at most one broken bond on a given timestep. It also means that if atom I chooses atom J as its sole partner, but atom J chooses atom K is its sole partner (due to Rjk > Rij), then this means atom I will not be part of a broken bond on this timestep, even if it has other possible bond partners.

The prob keyword can effect whether an eligible bond is actually broken. The fraction setting must be a value between 0.0 and 1.0. A uniform random number between 0.0 and 1.0 is generated and the eligible bond is only broken if the random number < fraction.

When a bond is broken, data structures within LAMMPS that store bond topology are updated to reflect the breakage. Likewise, if the bond is part of a 3-body (angle) or 4-body (dihedral, improper) interaction, that interaction is removed as well. These changes typically affect pairwise interactions between atoms that used to be part of bonds, angles, etc.

Note

One data structure that is not updated when a bond breaks are the molecule IDs stored by each atom. Even though one molecule becomes two molecules due to the broken bond, all atoms in both new molecules retain their original molecule IDs.

Computationally, each timestep this fix operates, it loops over all the bonds in the system and computes distances between pairs of bonded atoms. It also communicates between neighboring processors to coordinate which bonds are broken. Moreover, if any bonds are broken, neighbor lists must be immediately updated on the same timestep. This is to insure that any pairwise interactions that should be turned “on” due to a bond breaking, because they are no longer excluded by the presence of the bond and the settings of the special_bonds command, will be immediately recognized. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently.

You can dump out snapshots of the current bond topology via the dump local command.

Note

Breaking a bond typically alters the energy of a system. You should be careful not to choose bond breaking criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and break it when 2 atoms are separated by a distance far from the equilibribum bond length, then the 2 atoms will be dramatically released when the bond is broken. More generally, you may need to thermostat your system to compensate for energy changes resulting from broken bonds (and angles, dihedrals, impropers).


Restart, fix_modify, output, run start/stop, minimize info:

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.

This fix computes two statistics which it stores in a global vector of length 2, which can be accessed by various output commands. The vector values calculated by this fix are “intensive”.

These are the 2 quantities:

    1. # of bonds broken on the most recent breakage timestep
    1. cumulative # of bonds broken

No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

Default

The option defaults are prob = 1.0.